A user can choose to navigate the Database either alphabetically or by category. In the case of category, the entries in the encyclopedia can be accessed from an alphabetical list, a timeline of the series' in-game universe or a relationship tree (exclusively showing characters and affiliated groups). Articles will contain highlighted words which link to related articles, and the application itself keeps track of all articles viewed. By default, the Database locks all references to Metal Gear Solid 4 to safeguard against spoilers. In order to unlock this hidden information, the player must have a completed Metal Gear Solid 4 save file (and player data file, to ensure the save file was not downloaded). Even when fully unlocked it still contains minor gaps, and even the Database never fully explains everything.

The Database was the source of much controversy when it was first released, as it contained references to several events in the Metal Gear universe previously thought to be non-canon (such as confirming that the Snatcher project was not merely a rumor), leaving out some characters fates (such as Ivan Raikov, Python and the Beauty and the Beast Unit), omitting some events in some characters' lives (such as facts relating to Gray Fox's development), confusing some characters (such as claiming that it was Otacon's grandfather who was Aleksandr Leonovitch Granin's "American friend" when the Metal Gear Solid 3 voice casting sheet and Metal Gear Solid: Peace Walker proved that it was actually Otacon's father) and even contradicting certain events itself (such as mentioning that Raiden's memories from his time fighting in wars as a child were erased by Solidus Snake and that Solidus was the one who caused Arsenal Gear to crash into Manhattan as a last resort strike at the Patriots).

There was also some controversy over Liquid Ocelot's handling, as the Database makes vague hints in some articles suggesting that Liquid's personality was in control but subsequently contradicting this information saying it was an act all along in other articles. On a related note, although various information was hidden until having a complete player data and save file for Metal Gear Solid 4 to avoid spoilers, some information, such as the revelation that Liquid Ocelot had removed his arm (something that was never revealed nor hinted at until the final battle of Act 5), was shown prior to that despite it being unveiled around the same time as most of the other hidden information and thus being a major spoiler.

On the other hand, the Database also corrected some errors that were prevalent in the original sources. One example being that they correctly identified the award Holly White won for her documentary The Unknown Bloodshed as being an Emmy, instead of a Grammy (the latter being a music award), as it was identified in the Metal Gear 2 manual.